The Darker Doctor
by Queen Of The Lab01
Summary: You all know the story of The Master, he held the world captive, assasinated the president and tortured the Doctor to a point near his own death. But what if, somehow the doctor and the master's roles had been swtiched in the mind's of the world. Picture a world with a hero-The Master, and a villian-the Doctor. (Please review) No flames. (Also called the doctor and the master)
1. Chapter 1

**Hey, so just a quick note, this takes durring the time of the 10th Doctor (He is my favorite) and i really hope you all review cause puting out a new storty is a little scary. I would just like to know if people like the story! So please REVIEW!**

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Chapter One:

Have you ever had one of those days where it seems like absolutely nothing extraordinary is going to happen, and then…it does?

The day had begun normally; the doctor awoke on time, and was ready to travel through space and time. He was ready for another busy day of saving lives, helping the citizens of the universe, and making sure aliens didn't destroy time and space as we know it.

That's how the day started, that's how it always started.

He took a scan around the room, the interior of the TARDIS was…in six words; "it's bigger on the inside." The Doctor stopped a minute, and looked around the room—something felt really off all of a sudden. The TARDIS hummed, and spit as it always did, but it was louder, and the ride was unnaturally bumpy. The odd this was, the doctor could tell that it was moving, but he didn't remember ever setting off on any new adventures. Where was he going, and where was it taking him?

There was a sudden rush of turbulence, the ship shook and sputtered. The doctor was knocked off of his feet and on to his back, hitting his head on the floor. He got up, supporting his head with the palm of his hand.

"Now what was that?" he mumbled

He picked himself off of the floor, and stumbled over to the door. Slowly, he pushed the door open, and the blue sliding doors opened accordion style.

He popped his head out the door, and cocked his head back in surprise. For such odd circumstances, he had been expecting a foreign world he had never seen, or a moment in time he had yet to visit. But instead what he found was a dark alley way, lit by the late afternoon sun of London. He wasn't anywhere unfamiliar; he was in the one place where he had always felt most comfortable—earth.

As he stepped out of the TARDIS, and into the streets, it looked like London; it smelled like London, it even sounded like the bustling streets of London. But something felt very wrong, this place wasn't having the same calming effect it usually did, instead he felt worried and on edge.

He closed the doors of the TARDIS behind him.

"Hey you." A voice called, he began to turn around to face this voice when it yelled again, "No! Don't turn around; just give me your money."

He raised an eyebrow, "You want money?" he asked "that's funny usually when I meet people that try to rob me they want the box."

"The box? Why would I want a silly old police box?"

He chuckled

"No laughing!"

"Sorry, it's just funny how closed minded humans are, they can be facing the entire universe before them, and only want some paper in my pocket." He mused the idea "You are Human aren't you?" he asked just to be sure.

"Of course, now I said give me your money."

The doctor began to turn around, and the voice called a warning, but he didn't listen. What he saw next, surprised, and shocked him.

"Captain Jack?" he asked

The man nodded, but continued to squint at the Doctor, until he got a good view of his face. Then something flashed on his face, something like fear, something like unfiltered and pure terror, but it was only for a moment and disappeared as soon as it had come.

"you." He scowled

"Yeah me, who else do you know with a teleporting blue box?"

"Sorry, but your humor isn't going to get you out of this mess."

"What mess? What did I do now?" the Doctor laughed

Jack looked less than amused, "what have you done? More like what haven't you done!?"

"You're a monster." Jack said plainly

"Me? I believe you survived being left in the past, besides that was a long time ago."

"I don't know what you're talking about, but it's time for you to pay for your transgressions." Jack looked like he was ready to be sick, as if being in the very presence of the doctor made him physically ill. This was definitely odd, he had never thought that he had been overly nice to Jack, but he was positive he had never done anything "monstrous".

"What did I do to you?" the doctor asked honestly

"Me? Nothing, but the entire human race, lots and lots of stuff."

"The human race? I have done nothing but save the human race."

Jack almost laughed, it wasn't a good heartedly laugh as though this were some cruel joke, he laughed as though he couldn't believe the doctor's answer.

"How about the time you assassinated the president of America? And all of those innocent people you murdered."

"What? I have never killed anyone who was innocent."

"I don't really feel like listening to your twisted reasoning behind your kills, but I do feel an over whelming urge to kill you every time you open your mouth."

"Yikes sorry." He chortled; this had to be some kind of joke, right? "Wait? Assassinated the president, that wasn't me, what are you talking about Jack that was The Master."

"Don't you dare say a word against the master, he is a good man, and is nothing like you. You are an atrocious, disgusting slaughterer."

"Is this some kind of joke?" the doctor choked "and since when are you on the master's side?"

Jack's face twisted and distorted, "you at as though you don't even remember. You used you power, and abused your gifts. You tortured the master, and held the entire world hostage. "

The doctor began to recall this happening, but he remembered it exceptionally differently.

"I don't know what is happening here, but you have got this all wrong. I didn't kill anyone, I didn't hold anyone hostage, that was the master, I was the one he tortured. You were the one that came to save me, and Martha Jones, don't you remember?"

Jack almost considered this, but soon snapped out of his confusion. He reached to his wrist, and into his watch he reported: _Code Red! Alert be on high alert, Captain to torchwood, The Doctor is in sight, permission to kill._ There was no answer on the other end of the connection—just static.

Captain Jack looked up as if to say; what did you do?

He shrugged "I guess I will take that as a 'permission granted.'" With that he pulled out a gun, and pointed to barrel straight into the doctor's face.

"Night night Doc,"

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	2. Chapter 2

**I really hope that you all enjoy, and have as much fun reading this, as I have writing it! Please review! :)**

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Chapter Two:

"Whoa, lets slow down here Jackie boy." The doctor attempted

No such luck.

Captain jack's thumb slid back wards onto the firing mechanism and with a sharp the click the gun and jack prepared to fire. Deciding that there was no other choice, the doctor raised a finger to say something.

"If I may say one thing before you blast a hole in my head, might you give me the honor of one last command?"

Jack's eye brow started to creep exponentially in an upward direction.

"Well… you know, ah…Look!" he pointed his finger behind jack's head

Jack turned to see what it was that the doctor was pointing at, and when he did, the doctor took off. He sprinted down the surprisingly well lit street ally.

"Stop!" jacks voice called, and the steady click of the gun rang out again, this time followed by the loud crack of a gunshot. Before he could react, the doctor felt a hot tearing sensation in his chest, and a not so mysterious warm liquid running down his chest. He crumpled down onto the dirty concrete beneath him. The world around him blurred, and slowly faded into a consistent shade of black.

"Doctor?" a voice asked, it sounded muffled and distant almost as though he was hearing it from above water while he was below.

His feverish face felt cool, and refreshed all of a sudden, even the throbbing in his chest seemed to have dulled.

"Doctor," the voice called again, obviously waiting for answer "I need you to respond doctor."

He tried to answer, but he just heard a muffled *Blub*

With that he realized the pain in his chest, it was the reason that he hadn't felt his gunshot wound. The brain can only discern one pain at a time, and it chooses to let you feel the worst one of all. What was a worse pain than a gunshot wound? Airlessness, the doctor suddenly felt hyper aware of the dry, burning in his lungs, he had no air, he had no source of life, what he had heard as a *Blub* had indeed been him attempting to speak, his eyes shot open. The world around him looked distorted and odd, it seemed blurry and he soon realized why. He was underwater, this was why he couldn't breathe, and this was why he couldn't speak.

"Doctor," the voice mumbled again through the thick glass, this time it sounded playful, and almost as though it were taunting him.

"Help!" he tried to scream, it only came out as a series of bubbles and air pockets

He squirmed and shook as he tried to find a way out, there was no escape.

In front of the glass a face appeared, it was familiar and friendly, but also a cruel light shone in the eyes of the figure.

It was obviously a woman, she was medium height about 5'10'', she had light brown skin and dark hair pulled back neatly into a bun.

A single name came to mind as the doctor gazed upon her face: _Martha?_

He felt his eyes widen and the water began to sting his eyes. He thrashed about, reminded of his lack of air.

"Release him," she said, she flicked her hand like a spoiled child, in a very un-Martha like way. Her tone was bored, and she seemed to second guess her decision to release him because she didn't look very thrilled when the water began to drain. The water level shank, at first it reached his head, then his shoulders, and his hips, until it was gone and left only an existed Doctor in its wake. He desperately gasped for air, and when he finally got some into his empty lungs, his body went on high alert, his senses sharpened, and his chest no longer felt like a chunk had been ripped out.

He collapsed in a heap on the floor, his body soaking and shivering. He leaned against the wall behind him, began to catch his breath, while doing his best to look pathetic and harmless. Hopefully they wouldn't harm him while he looked like a shivering puppy out in the rain.

"So this is the Doctor?" Martha spoke

"Why?" he coughed

"Oh I don't know; revenge, for all of those innocent people you have killed."

He shook his head numbly, "No," the doctor was still wheezing breathlessly "I didn't do these things that you think I did,"

She squinted her eyes "Oh, I have several eye witnesses and a whole world full of people who might just disagree."

He didn't know what was going on; something must have gotten changed around somehow. Was he in a new dimension? Or had he created a paradox long ago, just recently fallen into it? Whatever it was, everyone seemed to think that he was guilty of all of the crimes that he had been sure the master had done. Where ever he was now, the master was the hero, and he was the villain. But still, there were still some factual errors, why would there be a "world full of people" who remembered this occurrence, he had wiped their memories, and rewound time so that none would have to live knowing the horrors that they had witnessed, then why hadn't the master when given the chance?

"Yeah, something is very wrong here, I really don't know what's going on here, but I can explain."

Martha scowled "This I have got to hear."

"Umm…well, I don't know how I got here, or what I am doing here, but this is all very wrong. I come from a universe where The Doctor is a hero loved by all, because he saves lives not ends them. But, also a world with a crazed maniac—The Master, who is actually a presidential assassinating, world hostage holding, government controlling madman, it's a tad different wouldn't you say?"

Martha looked stunned, he had expected her to laugh or something, but instead she just stared. She looked as though this made sense and somewhere deep down; she believed that the doctor was a good man, not scoundrel he was made out to be here. The look of belief was quickly overtaken by one of disbelief.

"Yeah right, that's a laugh, the doctor is and always will be a hideous psychopath," she looked deep into his eyes sternly. Then she turned to the guards and waved a hand dismissively "Get this _thing_ out of my sight, take him to the dungeons."

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	3. Chapter 3

Chapter Three:

"Let go of me," the doctor wheezed as they dragged him down a dark corridor down to what Martha had called 'the dungeon' scary enough that UNIT had a dungeon, but HE was being taken to it? Completely outrageous

Sadly his attempt at a mercy plea was in one word…ineffective. The laces to the doctor's converse sneakers were untied and dragging in the wet concrete potholes.

"Oi!" he exclaimed as the guards shoved him in through a wrought iron gate door. "Was that really necessary?"

Unsurprisingly, there was no response,

The doctor wasn't sure what he wanted to do, obviously something here was very wrong. But he didn't know how things got this way, was he in a new dimension or a paradox? Had someone been running around pretending to be him, copying the things that the master did in the year that never happened? It seemed plausible, but it still didn't explain why suddenly every one was so convinced that the master was the good guy here? He didn't know how, but he knew that he would find out that the master was tied into this as well, somehow he was at the source of all this, he had to be.

The doctor picked himself off of the floor, and dusted off his jacket. There were some stains on it from the mud and debris that would never come off however.

"Oh, well isn't this a surprise, just look who I happen to find here?" laughed a voice behind him. He couldn't put a finger on it, but he knew the voice, it was perky and smooth. Obviously this was a woman and obviously someone who was as familiar with him as he was her.

He turned to face her, and a shock induced shiver crawled up his body like little ants, biting and nipping him on the way up his legs.

"Cassandra?" he said in awe

But sure enough here she was, she should be dead he saw he be disintegrated twice actually—the memory that she was able to come back was not a source of great comfort for him. Her Caucasian skin stretched out on a canvas like taffy, and her face still intact two big blue eyes staring up at him.

"That's right darling, I am back."

He didn't know how to respond. He wanted to comeback with some brilliant and clever retort but instead he said: "but…your dead, I saw you died…twice."

She rolled her amethyst eyes at him, which admittedly gave him the creeps, because she was after all just a lump of skin.

"Oh come now, I feel like, how I came back is the least of our worries."

"Our?" the doctor choked "Since when have you ever been on my side?"

If she could be crossing her arms right now, she would be doing it now.

"Look, you obviously are as confused as I am right now; these people have absolutely no memory of certain key events that we both know happened." She winked at him.

"What do you mean by that?"

"Well that girl, Martha, she was there on the UNIT ship Valiant, and yet she remembers it all wrong."

"The year that never happened." The doctor whispered to himself "wait, how do you know about that?"

"Oh sweetie did you really not know? I was there, the entire time."

The idea that Cassandra had been on the valiant freaked the doctor out, he had never been so weak and so vulnerable, he liked things the way they were now, where no one but Martha and her family knew about his year of weakness, he was under all definitions of the word, ashamed.

"That's impossible," he said quite positive "we would have known, if you on board, we had a year to get to know the ship, do you really expect me to believe that you were on it the whole time, and that you have been back for so long? That's ridiculous!"

"Call it what you will doctor, but I have been inside you head Mister, so don't try to fool me, Mr. Last of the time lords."

"How did you get here?" he asked abruptly "In the dungeons I mean."

Right as she was about to answer, sarcastically it sounded like, they heard voices down the hall, and another prisoner in tote. The voice was obviously woman, and the doctor was positive that he knew the voice, who was she? It wasn't like him not to remember people, he could still to this day, and hundreds of years later still recite the names of every companion he had ever traveled with, even his dearest granddaughter. Then after he heard her say one more phrase it clicked for him:

"Won't you let go of me, if you don't mind."

"No. ma'am," they responded and he ducked under his door to avoid being seen by the guards, because surly if they knew he was across the way, they certainly wouldn't put her right next to him.

The door a crossed the way, screeched shut and with a hollow thud locked shaking the walls and the floor around and under him. He began to rise up from where he had been squatting on the floor to get a good look at her. He rose up slowly, peered through he bars at the top of the doors. Sure enough there she was, she was pacing around in her cell mumbling to herself. She was wearing a dark black woman's pant suit and her auburn hair was neatly brushed, combed and styled, just like always.

"Pssst." He hissed, blowing hair between his teeth.

He felt Cassandra behind him, probably wondering what the heck he was doing; he did after all look presumably quite daft.

But the woman turned and confidently asked "Who's there?"

She locked eyes with him, but her expression didn't light up the way that he had hoped. SH just stared for a few seconds, and asked again "Who's there, I am sorry but I am afraid that I don't know you sir."

Heartbrokenness. Maybe she had been arrested out of time, and this was a version of her that had not fought of slithen with him.

She raised a badge, for some presumably good reason they hadn't taken it from her "Harriet Jones former prime minister."

So she was a former prime minister, so they had met already.

"It's me Harriet, it's the doctor."

There last meeting hadn't gone so well, he had ended her career in politics and she shouldn't have ever forgiven him, but he was beyond all doubt happy to see her, in his world where ever it was, she was dead—killed by Daleks.

She raised an eye brow, and asked him a fairly simple and oh so complicated question: "Doctor Who?"

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